The two boys and four girls were among nine children aged between one and nine who were taken for baptism by two members of an apostolic church.
"Six juveniles died during baptism in Muriwo village in Mashonaland East (province) on Tuesday," police spokeswoman Charity Charamba said in a statement.
"We would like to warn members of the public to desist from engaging in dangerous practices under the guise of freedom of worship."
"After realising the children were dead, the culprits ran away from the scene but they were later arrested. They are being charged with culpable homicide."
Local media said those arrested were two women aged 30 and 34.
Apostolic churches and sects in Zimbabwe have grown in popularity in Zimbabwe, which has suffered from years of economic decline.
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